Mutagenetix > Incidental Mutation

Incidental Mutation 'R1996:Prdm5'

225737

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

040006-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1996 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 65913072 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 207 (Y207C)

Ref Sequence

ENSEMBL: ENSMUSP00000079979 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031973] [ENSMUST00000031976] [ENSMUST00000081219] [ENSMUST00000172638]

AlphaFold

Q9CXE0

Predicted Effect

probably damaging
Transcript: ENSMUST00000031973
AA Change: Y401C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: Y401C

Domain	Start	End	E-Value	Type
PDB:3EP0\|B	4	101	1e-11	PDB
Blast:SET	8	100	4e-64	BLAST
ZnF_C2H2	105	127	3.16e-3	SMART
ZnF_C2H2	133	155	8.81e-2	SMART
ZnF_C2H2	161	183	1.95e-3	SMART
ZnF_C2H2	189	211	6.78e-3	SMART
ZnF_C2H2	217	240	1.2e-3	SMART
ZnF_C2H2	246	268	4.87e-4	SMART
ZnF_C2H2	274	296	2.4e-3	SMART
ZnF_C2H2	302	324	2.43e-4	SMART
ZnF_C2H2	330	352	3.21e-4	SMART
ZnF_C2H2	358	380	1.45e-2	SMART
ZnF_C2H2	387	410	1.43e-1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000031976
AA Change: Y585C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: Y585C

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART
ZnF_C2H2	486	508	2.43e-4	SMART
ZnF_C2H2	514	536	3.21e-4	SMART
ZnF_C2H2	542	564	1.45e-2	SMART
ZnF_C2H2	571	594	1.43e-1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000081219
AA Change: Y207C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: Y207C

Domain	Start	End	E-Value	Type
Blast:SET	8	72	2e-34	BLAST
ZnF_C2H2	80	102	2.4e-3	SMART
ZnF_C2H2	108	130	2.43e-4	SMART
ZnF_C2H2	136	158	3.21e-4	SMART
ZnF_C2H2	164	186	1.45e-2	SMART
ZnF_C2H2	193	216	1.43e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000172638

SMART Domains

Protein: ENSMUSP00000133423
Gene: ENSMUSG00000029913

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205155

Meta Mutation Damage Score

0.1522

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.0%

Validation Efficiency

99% (84/85)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a hypomorphic allele display delayed bone ossification with reduced collagen fibril formation, total bone area, bone mineral content and bone mineral density. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	T	A	6: 121,646,556 (GRCm39)	W1069R	probably damaging	Het
Aaas	C	T	15: 102,248,494 (GRCm39)	V241I	probably benign	Het
Abca3	A	G	17: 24,606,506 (GRCm39)	E787G	probably damaging	Het
Abi3bp	A	T	16: 56,491,720 (GRCm39)	E582D	possibly damaging	Het
Adam21	A	G	12: 81,606,376 (GRCm39)	M462T	possibly damaging	Het
Alox12e	T	C	11: 70,207,034 (GRCm39)	T591A	probably benign	Het
Ankmy2	T	C	12: 36,243,796 (GRCm39)	M337T	probably benign	Het
Antxrl	A	G	14: 33,797,786 (GRCm39)	N587S	probably benign	Het
Apol6	T	A	15: 76,934,956 (GRCm39)	I75N	probably benign	Het
Atad2b	A	T	12: 5,040,883 (GRCm39)	H184L	probably benign	Het
Atf6b	A	T	17: 34,871,961 (GRCm39)		probably null	Het
B3gnt4	G	A	5: 123,649,402 (GRCm39)	V256I	probably damaging	Het
BC034090	C	T	1: 155,097,340 (GRCm39)		probably benign	Het
Bend4	C	A	5: 67,557,527 (GRCm39)	V430F	probably damaging	Het
Camkv	A	G	9: 107,824,320 (GRCm39)	D244G	probably damaging	Het
Caps2	T	A	10: 112,039,908 (GRCm39)	L450Q	probably damaging	Het
Ccr1	T	A	9: 123,763,551 (GRCm39)	K326N	probably benign	Het
Cep135	T	C	5: 76,780,113 (GRCm39)	I815T	probably benign	Het
Chchd4	A	G	6: 91,442,116 (GRCm39)	Y101H	probably damaging	Het
Copb1	G	C	7: 113,831,438 (GRCm39)	A570G	probably benign	Het
Cpsf2	C	A	12: 101,964,867 (GRCm39)	T505K	probably benign	Het
Cwf19l2	A	G	9: 3,417,947 (GRCm39)	R136G	probably benign	Het
Daxx	A	G	17: 34,132,585 (GRCm39)	T572A	possibly damaging	Het
Etaa1	C	A	11: 17,902,671 (GRCm39)	D89Y	probably damaging	Het
Ezhip	GTCATCATCATCATC	GTCATCATCATCATCATC	X: 5,994,645 (GRCm39)		probably benign	Het
Fchsd2	T	C	7: 100,927,660 (GRCm39)	F701L	probably benign	Het
Fstl5	A	T	3: 76,615,141 (GRCm39)	H734L	probably benign	Het
Gabbr1	T	A	17: 37,380,112 (GRCm39)	W584R	probably damaging	Het
Galc	T	C	12: 98,218,285 (GRCm39)	D189G	probably damaging	Het
Gm9979	T	C	13: 40,859,228 (GRCm39)		noncoding transcript	Het
Grin2b	T	C	6: 136,021,209 (GRCm39)	S31G	possibly damaging	Het
Gtf2ird1	T	C	5: 134,405,740 (GRCm39)		probably benign	Het
Hoxc4	T	C	15: 102,944,183 (GRCm39)	I187T	probably damaging	Het
Hsd3b6	A	T	3: 98,713,597 (GRCm39)	I234N	probably damaging	Het
Ifit3b	T	C	19: 34,588,877 (GRCm39)	C18R	probably damaging	Het
Igdcc4	T	A	9: 65,029,101 (GRCm39)	V246E	probably damaging	Het
Il1rap	A	T	16: 26,541,243 (GRCm39)	T495S	probably benign	Het
Kctd19	T	C	8: 106,121,932 (GRCm39)	E205G	probably null	Het
Kif21a	A	T	15: 90,878,574 (GRCm39)	C235*	probably null	Het
Krt16	A	T	11: 100,139,614 (GRCm39)	S35T	unknown	Het
Lamc2	T	C	1: 153,030,216 (GRCm39)	D142G	possibly damaging	Het
Larp4	G	T	15: 99,882,844 (GRCm39)	W22L	probably damaging	Het
Ldlrad1	C	T	4: 107,072,158 (GRCm39)	R127*	probably null	Het
Mamdc2	G	A	19: 23,341,289 (GRCm39)	Q229*	probably null	Het
Mbtd1	CT	CTT	11: 93,823,222 (GRCm39)		probably null	Het
Msln	T	A	17: 25,973,193 (GRCm39)	M1L	possibly damaging	Het
Mtch2	T	C	2: 90,677,665 (GRCm39)	V8A	possibly damaging	Het
Nav3	A	T	10: 109,689,262 (GRCm39)	N338K	probably damaging	Het
Or10x4	T	C	1: 174,218,983 (GRCm39)	M116T	probably damaging	Het
Or51a39	A	G	7: 102,362,999 (GRCm39)	L207P	probably damaging	Het
Or6c5	C	A	10: 129,074,298 (GRCm39)	N93K	possibly damaging	Het
Otof	A	G	5: 30,578,381 (GRCm39)	V89A	probably benign	Het
Phka2	T	C	X: 159,324,411 (GRCm39)	I255T	probably benign	Het
Pias2	T	C	18: 77,216,759 (GRCm39)		probably null	Het
Pja2	T	A	17: 64,594,639 (GRCm39)		probably null	Het
Plxnb2	C	T	15: 89,042,971 (GRCm39)	V1473I	probably benign	Het
Pnpt1	T	A	11: 29,091,679 (GRCm39)	D363E	probably benign	Het
Rexo5	T	A	7: 119,423,080 (GRCm39)	V304E	probably damaging	Het
Robo1	G	T	16: 72,767,067 (GRCm39)	R413L	probably benign	Het
Rsf1	G	A	7: 97,313,839 (GRCm39)	E864K	probably damaging	Het
Scap	C	T	9: 110,202,039 (GRCm39)		probably benign	Het
Scn8a	T	A	15: 100,922,260 (GRCm39)	M1311K	probably damaging	Het
Slc28a2	A	T	2: 122,286,043 (GRCm39)	I460F	probably damaging	Het
Smco1	A	G	16: 32,092,730 (GRCm39)	R134G	probably benign	Het
Spopfm1	A	T	3: 94,173,018 (GRCm39)	M9L	probably benign	Het
Sspo	A	G	6: 48,452,424 (GRCm39)	E2651G	possibly damaging	Het
Stab2	T	C	10: 86,838,895 (GRCm39)	N57S	probably damaging	Het
Tenm3	C	A	8: 48,681,703 (GRCm39)	Q2642H	probably damaging	Het
Thsd7b	G	T	1: 129,686,188 (GRCm39)	E577*	probably null	Het
Tlr3	A	G	8: 45,850,734 (GRCm39)	V721A	probably benign	Het
Tnik	A	G	3: 28,719,829 (GRCm39)	I1226V	probably damaging	Het
Traf3	A	G	12: 111,227,095 (GRCm39)	K328E	probably benign	Het
Tyw1	T	A	5: 130,291,652 (GRCm39)		probably benign	Het
Vmn1r213	T	G	13: 23,196,473 (GRCm39)	V352G	probably benign	Het
Vmn2r111	T	C	17: 22,767,062 (GRCm39)	I812V	probably benign	Het
Vmn2r26	A	G	6: 124,038,144 (GRCm39)	N573S	probably damaging	Het
Vmn2r45	G	A	7: 8,475,024 (GRCm39)	T668I	probably damaging	Het
Zbtb20	T	A	16: 43,430,443 (GRCm39)	V318E	probably damaging	Het
Zc2hc1c	A	G	12: 85,343,434 (GRCm39)	R524G	probably benign	Het
Zc3h18	C	G	8: 123,134,126 (GRCm39)		probably benign	Het
Zfp618	T	C	4: 63,049,452 (GRCm39)		probably null	Het

Other mutations in Prdm5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01395:Prdm5	APN	6	65,847,374 (GRCm39)	missense	possibly damaging	0.93
IGL02363:Prdm5	APN	6	65,771,303 (GRCm39)	missense	probably damaging	1.00
IGL02457:Prdm5	APN	6	65,858,100 (GRCm39)	missense	probably damaging	1.00
IGL03190:Prdm5	APN	6	65,833,116 (GRCm39)	splice site	probably benign
IGL03239:Prdm5	APN	6	65,863,062 (GRCm39)	splice site	probably benign
IGL03377:Prdm5	APN	6	65,836,457 (GRCm39)	missense	possibly damaging	0.93
R0329:Prdm5	UTSW	6	65,839,887 (GRCm39)	splice site	probably benign
R0926:Prdm5	UTSW	6	65,860,531 (GRCm39)	missense	probably damaging	0.99
R1458:Prdm5	UTSW	6	65,860,585 (GRCm39)	missense	probably damaging	0.99
R1859:Prdm5	UTSW	6	65,808,263 (GRCm39)	missense	probably benign	0.03
R1956:Prdm5	UTSW	6	65,913,060 (GRCm39)	missense	probably damaging	1.00
R1997:Prdm5	UTSW	6	65,913,072 (GRCm39)	missense	probably damaging	1.00
R2019:Prdm5	UTSW	6	65,808,340 (GRCm39)	missense	probably damaging	0.99
R3082:Prdm5	UTSW	6	65,913,069 (GRCm39)	missense	probably damaging	1.00
R3819:Prdm5	UTSW	6	65,913,041 (GRCm39)	missense	possibly damaging	0.92
R4411:Prdm5	UTSW	6	65,878,771 (GRCm39)	nonsense	probably null
R4981:Prdm5	UTSW	6	65,847,446 (GRCm39)	missense	probably damaging	0.99
R5077:Prdm5	UTSW	6	65,756,158 (GRCm39)	missense	probably damaging	0.97
R5089:Prdm5	UTSW	6	65,833,074 (GRCm39)	missense	probably benign	0.01
R5138:Prdm5	UTSW	6	65,833,086 (GRCm39)	nonsense	probably null
R5735:Prdm5	UTSW	6	65,904,974 (GRCm39)	missense	possibly damaging	0.93
R6355:Prdm5	UTSW	6	65,860,578 (GRCm39)	missense	probably damaging	1.00
R6743:Prdm5	UTSW	6	65,860,635 (GRCm39)	missense	probably damaging	1.00
R6769:Prdm5	UTSW	6	65,839,920 (GRCm39)	missense	probably damaging	0.98
R7216:Prdm5	UTSW	6	65,904,967 (GRCm39)	nonsense	probably null
R7305:Prdm5	UTSW	6	65,808,244 (GRCm39)	missense	possibly damaging	0.83
R7510:Prdm5	UTSW	6	65,904,976 (GRCm39)	missense	probably damaging	0.97
R8270:Prdm5	UTSW	6	65,913,058 (GRCm39)	missense	probably damaging	1.00
R8529:Prdm5	UTSW	6	65,878,829 (GRCm39)	missense	probably damaging	1.00
R8856:Prdm5	UTSW	6	65,860,569 (GRCm39)	missense	possibly damaging	0.80
R9283:Prdm5	UTSW	6	65,858,060 (GRCm39)	missense	probably damaging	0.98
R9427:Prdm5	UTSW	6	65,771,321 (GRCm39)	missense	possibly damaging	0.65
R9477:Prdm5	UTSW	6	65,771,342 (GRCm39)	missense	possibly damaging	0.48
X0017:Prdm5	UTSW	6	65,846,246 (GRCm39)	missense	possibly damaging	0.94

Predicted Primers

PCR Primer
(F):5'- GTTCTTAGACCCACTAGCACATAC -3'
(R):5'- ATAGGCACATAAACACTGTCAGATC -3'

Sequencing Primer
(F):5'- CCACTAGCACATACTTGATAGAAGG -3'
(R):5'- GTCAGATCAATGAATCCTTTGTGGC -3'

Posted On

2014-08-25